week3section - Week 3 OH Wednesday 11-12pm PSB Room 2161...

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Week 3 OH: Wednesday 11-12pm, PSB Room# 2161
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Sequence-specific DNA binding proteins A) Transcripition Factors B) Restriction Endonuclease Non-sequence specific A) Histones (DNA packaging)
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Leucine Zipper •In eukaryotic transcription factors such as yeasts protein GCN4, contains Leu at every 7 th position. •Leucine zipper assists in dimerization of certain DNA-binding protein but are not themselves DNA-binding motifs.
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Zinc-Finger DNA-Binding Motifs •Predominantly eukaryotic DNA-binding Transcription Factor •Contains two Cys residues and two His residues •Each Zn 2+ ion, tetrahedrally liganded by Cys and His residues •Cys 2 - His 2 zin finger resembles prokaryotic HTH motif. •In yeast, Zinc finger assists DNA binding of protein GAL4, activated galatose-metabolizing enzymes
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Restriction Endonucleases Restriction Endonuclease recognize palindromic DNA sequence~4-8 base pairs Cleave DAN at specific sites that have not yet been methylated by the host’s modification methylase
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Non-specific DNA binding protein 1. There are 5 major types of histone protein: H2A, H2B,H3, H4, and H1. 2. Histone proteins are very basic (rich in basic amino acids) and highly conserved in evolution, except H1.structure/function of the packaged DNA. 3. Histone proteins form an octamer around which DNA is wound: 2x H2A , 2x H2B , 2x H3 , and 2x H4 . These are the “core histones.” 4. The histone octamer plus DNA is the nucleosome. H1 may cap this nucleosome. 5. There are histone variants for some of the histones, that may exchange within the nucleosome to change the
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Limited nuclease digestion of chromatin to release nucleosomes and identify components
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Histone Modification 1. + charged lysines keep nucleosomes compact 2. Acetylation of lysines removes + charge. Chromatin less condensed. (HATs and HDACs) 3. Specialized Proteins can bind to acetylated histone tails 4. Other modifications that affect DNA compaction: methylation phosphorylation ubiquitination
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DNA Replication http://www.youtube.com/watch?v=teV62zrm2P0&feature=related http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html
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DNA Replication
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the DNA strands are antiparallel, and replication proceeds in the 5' to 3' direction on EACH strand
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